Panel of normals for Mutect2 GRCh37
Hello,
I plan on using Mutect2 to call somatic variants for WGS. The alignment and sorting is already performed by the core facility, which uses the GRCh37.p13 reference genome. For optimal performance a panel of normals should be used when running Mutect2, however as far as I know there is no publicly available panel of normals for the GRCh37. However, there is a panel of normals for b37 (https://console.cloud.google.com/storage/browser/_details/gatk-best-practices/somatic-b37/Mutect2-WGS-panel-b37.vcf). I was wondering if you think, that I can take this panel of normal, regardless of the slight differences ( https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies) in the reference genome.
Cheers!
-
Hi nhaus,
The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.
We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.
For context, check out our support policy.
-
nhaus Go ahead and use our b37 panel on GrCh37 data. We do that all the time!
Please sign in to leave a comment.
2 comments